CiteFuse

DOI: 10.18129/B9.bioc.CiteFuse    

This is the development version of CiteFuse; for the stable release version, see CiteFuse.

CiteFuse: multi-modal analysis of CITE-seq data

Bioconductor version: Development (3.12)

CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

Author: Yingxin Lin [aut, cre], Hani Kim [aut]

Maintainer: Yingxin Lin <yingxin.lin at sydney.edu.au>

Citation (from within R, enter citation("CiteFuse")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CiteFuse")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CiteFuse")

 

HTML R Script CiteFuse
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0)
Imports SingleCellExperiment(>= 1.8.0), SummarizedExperiment(>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, SNFtool, propr, uwot, Rtsne, S4Vectors(>= 0.24.0), igraph, scales, scran(>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang
LinkingTo
Suggests knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle
SystemRequirements
Enhances
URL
BugReports https://github.com/SydneyBioX/CiteFuse/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CiteFuse_1.1.0.tar.gz
Windows Binary CiteFuse_1.1.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) CiteFuse_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CiteFuse
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CiteFuse
Package Short Url https://bioconductor.org/packages/CiteFuse/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: